Israel gave strong indications today that its forces had secretly sabotaged some of the ships bound for Gaza as part of the freedom flotilla.

Matan Vilnai, the deputy defence minister, was asked on Israel Radio whether there had not been a smarter alternative to direct assault. He answered that "all possibilities had been considered," adding: "The fact is that there were less than the 10 ships that were due to participate in the flotilla."

The comments appeared to dovetail with reports that two of the vessels malfunctioned at the same time and in the same way. Challenger I and Challenger II, carrying 36 activists, were forced into port in Cyprus on Friday evening when steering systems on both ships broke down on the passage from Heraklion in Crete, a campaign spokeswoman said.

Challenger II also started taking on water after the bilge pump suddenly stopped working and an inspection yesterday revealed "very suspicious" faults, according to Greta Berlin, a spokeswoman for Free Gaza.

An unnamed Israeli Defence Force source who briefed the Knesset's foreign affairs and defence committee on the widely criticised armed interception of the flotilla at sea, also spoke of "grey operations" being mounted against the flotilla. No further detail was reported, probably because of the military censorship rules binding the Israeli media.

Both were forced to radio distress signals to Cypriot ports and Berlin said the captain of Challenger I, Denis Healey, was "frightened that he was not going to be able to get the boat in".

"They had mechanical probles on Friday afternoon at around 3.30pm when they were going towards Cyprus to pick people up. They had been travelling from Crete and had been at sea for about 30 hours," she said.

Once in port in northern Cyprus, Healey had to repair hydraulic lines on the vessel. Challenger II had to pull alongside the main Turkish ship, the Mavi Marmara, on the high seas 70 miles off Cyprus, to transfer its passengers before it limped into port.

The unnamed Israeli officer also said that military planners had considered trying to stop the Mavi Marmara rather than board it but had decided against it because the Turkish ship was too fast.

There is at least one precedent for naval sabotage by the Israelis. Flotilla 13, the elite naval commando unit that carried out Monday's raid, reportedly blew up a ship named al-Awda (the Return) which was chartered by the PLO in 1988 to dramatise the plight of Palestinian refugees. It sank in Limassol harbour, Cyprus.